Intraspecific Arabidopsis Hybrids Show Different Patterns of Heterosis Despite the Close Relatedness of the Parental Genomes

130

101

Hybrid rice is the dominant form of rice planted in China, and its use has extended worldwide since the 1970s. It offers great yield advantages and has contributed greatly to the world’s food security. However, the molecular mechanisms underlying heterosis have remained a mystery. In this study we integrated genetics and omics analyses to determine the candidate genes for yield heterosis in a model two-line rice hybrid system, Liang-you-pei 9 (LYP9) and its parents. Phenomics study revealed that the better parent heterosis (BPH) of yield in hybrid is not ascribed to BPH of all the yield components but is specific to the BPH of spikelet number per panicle (SPP) and paternal parent heterosis (PPH) of effective panicle number (EPN). Genetic analyses then identified multiple quantitative trait loci (QTLs) for these two components. Moreover, a number of differentially expressed genes and alleles in the hybrid were mapped by transcriptome profiling to the QTL regions as possible candidate genes. In parallel, a major QTL for yield heterosis, rice heterosis 8 (RH8), was found to be the DTH8/Ghd8/LHD1 gene. Based on the shared allelic heterozygosity of RH8 in many hybrid rice cultivars, a common mechanism for yield heterosis in the present commercial hybrid rice is proposed.

Section: Significancementioning

confidence: 78%

Section: Significancementioning

confidence: 91%

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

Huang

Song

et al. 2016

130

101

“…In crosses between the C24 and Ler ecotypes, the F1 hybrids had substantial levels of hybrid vigor in vegetative biomass of the rosette and reproductive yields of seed production (13). At 15 d after sowing (DAS), the vegetative biomass of the F1 hybrids was ∼26% greater than the biomass of the better parent, and at 28 DAS, the F1 biomass had increased to ∼90% greater than the better parent ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Hybrid mimics and hybrid vigor in Arabidopsis

Wang

Greaves

Groszmann

et al. 2015

Self Cite

F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.I n Arabidopsis some ecotypes with similar genome sequences produce F1 hybrids with large increases in vegetative and reproductive yields (1, 2). These results appear to be at variance with the generalization that the larger the genetic distance between parents, the greater the hybrid vigor (3); however, the Arabidopsis ecotypes have different epigenomes that may be important for hybrid vigor (4). In hybrids between C24 and Ler, we found altered levels in two epigenetic systems: 24nt siRNAs and DNA methylation (4, 5). These epigenetic changes appear common among hybrid systems with similar observations being made in maize and rice hybrids (6). The epigenetic changes can correlate with changes in gene expression and contribute to the unique gene expression profile of the F1 hybrid (7). Not all crosses result in hybrid vigor (heterosis); some result in decreased vigor and yield referred to as "hybrid weakness" (8).Heterotic F1 hybrids are featured in agricultural and horticultural crops, and in all species, the yield gains are restricted to the F1 generation. The F2 and subsequent selfed generations are discarded because of reduced yields and heterogeneity of morphological and developmental traits. A hybrid crop system requires an efficient method of F1 hybrid seed production dependent on male sterility in the female parent and synchronous flowering of the male and female parents.QTL analysis in maize and rice has confirmed that hundreds of genome segments contribute to the heterotic phenotype, but the main m...

“…The F1 hybrid produced by crossing C24 and Landsberg erecta (Ler) accessions had substantial hybrid vigor in both biomass and seed yield phenotypes (6). The phenotype of the heterozygous F1 hybrid is highly uniform, but there were several phenotypes in the F2 population.…”

Section: Resultsmentioning

confidence: 99%

“…The F1 hybrids from crosses of the C24 and Ler ecotypes have a high level of hybrid vigor (heterosis) with uniform phenotypes in plant biomass (6). Recurrent selection of the phenotypes displayed by individual F2 plants produced F6 plants with phenotypes resembling the selected individual F2 plants.…”

Section: Discussionmentioning

confidence: 99%

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

Wang

Greaves

et al. 2017

Self Cite

F1 hybrids in Arabidopsis and crop species are uniform and high yielding. The F2 generation loses much of the yield advantage and the plants have heterogeneous phenotypes. We generated pure breeding hybrid mimic lines by recurrent selection and also selected a pure breeding small phenotype line. The hybrid mimics are almost completely homozygous with chromosome segments from each parent. Four particular chromosomal segments from C24 and 8 from Ler were present in all of the hybrid mimic lines, whereas in the F6 small phenotype line, the 12 segments were each derived from the alternative parent. Loci critical for promoting hybrid vigor may be contained in each of these 12 conserved segments. We have identified genes with similar altered expression in hybrid mimics and F1 plants but not in the small phenotype line. These genes may be critical for the generation of hybrid vigor. Analysis of transcriptomes indicated that increased expression of the transcription factor PHYTOCHROME-INTERACTING FACTOR (PIF4) may contribute to hybrid vigor by targeting the auxin biosynthesis gene YUCCA8 and the auxin signaling gene IAA29. A number of auxin responsive genes promoting leaf growth were up-regulated in the F1 hybrids and hybrid mimics, suggesting that increased auxin biosynthesis and signaling contribute to the hybrid phenotype. The hybrid mimic seeds had earlier germination as did the seeds of the F1 hybrids, indicating cosegregation of the genes for rosette size and the germination trait. Early germination may be an indicator of vigorous hybrids.heterosis | transcription factor | biomass | transregulation | germination T wo features common to hybrids in many crops are the increased yield and phenotypic uniformity of the F1 hybrid generation and the reduced yield and phenotypic heterogeneity of the F2 generation (1). These characteristics also apply to the F1 and F2 populations in Arabidopsis hybrids (2). The processes of capture of light and assimilation of CO 2 into photosynthate are the same in the hybrid and parents and as the hybrids have larger leaves than their parents, they produce more photosynthate (3).In a previous paper (2), transcriptome analyses showed that in the hybrids, most genes are expressed at the same levels as in the parents. Compared with the average level of gene expression in the parents, ∼2,000 genes (6% of the genome) have altered expression in the hybrids and are likely to be involved in the generation of the hybrid vigor phenotype. Many of the differentially expressed genes (DEGs) encode proteins in key metabolic pathways such as the plant hormone systems auxin and salicylic acid (SA) and the basal defense response, suggesting that these pathways contribute to the development of hybrid vigor (4). Altered hormone abscisic acid (ABA) and defense response have also been reported in rice hybrids (5). Despite the contrasting phenotypes of the F1 and F2 populations, we were able to develop "pure breeding" F5/F6 lines with phenotypes comparable to the F1 hybrids (hybrid mimics) (2). The hybrid mimic...